/***************************************************************************
 *   Copyright (C) 2007 by Alexandre Masselot,,,   *
 *   alex@alex-laptop   *
 *                                                                         *
 *   This program is free software; you can redistribute it and/or modify  *
 *   it under the terms of the GNU Library General Public License as       *
 *   published by the Free Software Foundation; either version 2 of the    *
 *   License, or (at your option) any later version.                       *
 *                                                                         *
 *   This program is distributed in the hope that it will be useful,       *
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
 *   GNU General Public License for more details.                          *
 *                                                                         *
 *   You should have received a copy of the GNU Library General Public     *
 *   License along with this program; if not, write to the                 *
 *   Free Software Foundation, Inc.,                                       *
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/
#ifndef ENZYME_H
#define ENZYME_H
#include "peptide.h"
#include <vector>
/**
  a virtual class as a basis for cleaving mechanism
	@author Alexandre Masselot,,, <alex@alex-laptop>
*/
namespace bol{
class Enzyme{
private:
  string m_name;
public:
    Enzyme();

    ~Enzyme();

  void setName(const string& theValue) {
      m_name = theValue;
  }
  
  /**
   * 
   * @return the name of the enzyme
   */
  string name() const {
      return m_name;
  }

  /**
   * get the cleavage position (no terminal)
   * @param src the original peptide
   * @param vpos vector of position where the peptide should be cleaved
   */
  virtual void cleavePositions(const Peptide& src, vector<int>&vpos)=0;

  /**
   * 
   * @param src the original sequence to be cleaved
   * @param vpept the list of cleaved peptide
   */
  void cleave(const Peptide& src, vector<Peptide>&vpept);

};
}
#endif
